ID:RPA49_HUMAN DESCRIPTION: RecName: Full=DNA-directed RNA polymerase I subunit RPA49; Short=RNA polymerase I subunit A49; AltName: Full=DNA-directed RNA polymerase I subunit E; AltName: Full=RNA polymerase I-associated factor 1; AltName: Full=RNA polymerase I-associated factor 53; FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Appears to be involved in the formation of the initiation complex at the promoter by mediating the interaction between Pol I and UBTF/UBF (By similarity). SUBUNIT: Component of the RNA polymerase I (Pol I) complex consisting of at least 13 subunits (By similarity). Interacts with PAF49/CD3EAP. Also binds UBTF/UBF (By similarity). SUBCELLULAR LOCATION: Nucleus, nucleolus. SIMILARITY: Belongs to the eukaryotic RPA49/POLR1E RNA polymerase subunit family.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
Pfam Domains: PF06870 - A49-like RNA polymerase I associated factor
ModBase Predicted Comparative 3D Structure on Q9GZS1
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
BC014331 - Homo sapiens polymerase (RNA) I polypeptide E, 53kDa, mRNA (cDNA clone MGC:22869 IMAGE:4042929), complete cds. AK302345 - Homo sapiens cDNA FLJ60956 complete cds, highly similar to DNA-directed RNA polymerase I-associated factor 53 kDa subunit (EC 2.7.7.6). AK303167 - Homo sapiens cDNA FLJ54770 complete cds, highly similar to DNA-directed RNA polymerase I-associated factor 53 kDa subunit (EC 2.7.7.6). AK023452 - Homo sapiens cDNA FLJ13390 fis, clone PLACE1001238, moderately similar to Mouse mRNA for RNA polymerase I associated factor (PAF53). AK301347 - Homo sapiens cDNA FLJ54187 complete cds, highly similar to Homo sapiens polymerase (RNA) I associated factor 1 (PRAF1), mRNA. AK024032 - Homo sapiens cDNA FLJ13970 fis, clone Y79AA1001533, moderately similar to Mouse mRNA for RNA polymerase I associated factor (PAF53). AK225050 - Homo sapiens mRNA for RNA polymerase I associated factor 53 variant, clone: adSE00728. BC017766 - Homo sapiens polymerase (RNA) I polypeptide E, 53kDa, mRNA (cDNA clone IMAGE:4695468). BC001337 - Homo sapiens polymerase (RNA) I polypeptide E, 53kDa, mRNA (cDNA clone MGC:5609 IMAGE:3461710), complete cds. CR457313 - Homo sapiens full open reading frame cDNA clone RZPDo834F0113D for gene PAF53, RNA polymerase I associated factor 53; complete cds, incl. stopcodon. KJ906297 - Synthetic construct Homo sapiens clone ccsbBroadEn_15967 POLR1E gene, encodes complete protein. AK091294 - Homo sapiens cDNA FLJ33975 fis, clone DFNES2002817, moderately similar to Mouse mRNA for RNA polymerase I associated factor (PAF53). AX746899 - Sequence 424 from Patent EP1308459. AB528033 - Synthetic construct DNA, clone: pF1KB0437, Homo sapiens POLR1E gene for polymerase (RNA) I polypeptide E, 53kDa, without stop codon, in Flexi system. JD462204 - Sequence 443228 from Patent EP1572962. DQ581828 - Homo sapiens piRNA piR-49940, complete sequence. JD543719 - Sequence 524743 from Patent EP1572962. JD098245 - Sequence 79269 from Patent EP1572962. JD182872 - Sequence 163896 from Patent EP1572962. JD212352 - Sequence 193376 from Patent EP1572962. JD212353 - Sequence 193377 from Patent EP1572962. JD197745 - Sequence 178769 from Patent EP1572962. JD412686 - Sequence 393710 from Patent EP1572962. JD412687 - Sequence 393711 from Patent EP1572962. JD512634 - Sequence 493658 from Patent EP1572962. JD512635 - Sequence 493659 from Patent EP1572962. JD561355 - Sequence 542379 from Patent EP1572962. JD127896 - Sequence 108920 from Patent EP1572962. JD308839 - Sequence 289863 from Patent EP1572962. JD444201 - Sequence 425225 from Patent EP1572962. JD135534 - Sequence 116558 from Patent EP1572962. JD145112 - Sequence 126136 from Patent EP1572962. JD325409 - Sequence 306433 from Patent EP1572962. JD533048 - Sequence 514072 from Patent EP1572962. JD431166 - Sequence 412190 from Patent EP1572962. JD532777 - Sequence 513801 from Patent EP1572962. JD444858 - Sequence 425882 from Patent EP1572962. JD073131 - Sequence 54155 from Patent EP1572962. JD073132 - Sequence 54156 from Patent EP1572962. JD201744 - Sequence 182768 from Patent EP1572962. JD165369 - Sequence 146393 from Patent EP1572962. JD046133 - Sequence 27157 from Patent EP1572962. JD114865 - Sequence 95889 from Patent EP1572962. JD251483 - Sequence 232507 from Patent EP1572962. JD078435 - Sequence 59459 from Patent EP1572962.
Biochemical and Signaling Pathways
Reactome (by CSHL, EBI, and GO)
Protein Q9GZS1 (Reactome details) participates in the following event(s):
R-HSA-73865 Assembly of RNA Polymerase I Holoenzyme (human) R-HSA-73757 Binding of RRN3 to RNA Polymerase I R-HSA-5250947 B-WICH complex binds rDNA promoter R-HSA-73758 Recruitment of Active RNA Polymerase I to SL1:phos.UBF-1:rDNA Promoter R-HSA-74994 Polymerase I Transcription Complex/Nascent Pre rRNA Complex pauses at the TTF-I:Sal Box R-HSA-73769 Loss of Rrn3 from RNA Polymerase I promoter escape complex R-HSA-74992 Dissociation of PTRF:Polymerase I/Nascent Pre rRNA Complex:TTF-I:Sal Box R-HSA-5250930 B-WICH recruits histone acetyltransferases R-HSA-74993 PTRF Binds the Polymerase I Transcription Complex/Nascent Pre rRNA Complex paused at the TTF-I:Sal Box R-HSA-74986 Elongation of pre-rRNA transcript R-HSA-427366 Transcription of intergenic spacer of the rRNA gene R-HSA-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9 R-HSA-73762 RNA Polymerase I Transcription Initiation R-HSA-5250924 B-WICH complex positively regulates rRNA expression R-HSA-73854 RNA Polymerase I Promoter Clearance R-HSA-73863 RNA Polymerase I Transcription Termination R-HSA-73772 RNA Polymerase I Promoter Escape R-HSA-5250913 Positive epigenetic regulation of rRNA expression R-HSA-73864 RNA Polymerase I Transcription R-HSA-73777 RNA Polymerase I Chain Elongation R-HSA-427413 NoRC negatively regulates rRNA expression R-HSA-212165 Epigenetic regulation of gene expression R-HSA-74160 Gene expression (Transcription) R-HSA-5250941 Negative epigenetic regulation of rRNA expression
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Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
